Effect of elastic energy on the folding of an RNA hairpin

Thomas, Neil; Imafuku, Yasuhiro

doi:10.1016/j.jtbi.2012.07.021

Cited by 4 publications

(6 citation statements)

References 30 publications

(70 reference statements)

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“…The inserts in Figs. 17(a) and 17(b) show samples of the trajectories for single elements computed from (21).…”

Section: B Bundle Of Hs Elementsmentioning

confidence: 99%

“…In fact, the importance of the topology of interconnections among the bonds and the link between the collective nature of the unfolding and the dominance of the HS-type parallel bonding have been long stressed in the studies of protein folding [104]. The broad applicability of the HS mechanical perspective on collective conformational changes is also corroborated by the fact that proteins and nucleic acids exhibit negative stiffness and behave differently in soft and hard devices [18,20,21].…”

Section: Nonmuscle Systemsmentioning

confidence: 99%

“…Almost identical descriptions of mechanically driven conformational changes were proposed independently in the studies of cell adhesion [8,9] and in the context of hair cell gating [10,11]. Other closely related systems include mechanical denaturation of RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) hairpins [12][13][14], unzipping of biological macromolecules [15][16][17][18][19][20][21], collective action of SNARE (soluble N-ethylmaleimide sensitive receptor) proteins during opening of synaptic pores [22] and even formation of ripples in graphene sheets [23]. For all these systems the HS model can be viewed as a fundamental mean-field prototype.…”

Section: Introductionmentioning

confidence: 97%

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Statistical mechanics of the Huxley-Simmons model

Caruel

Truskinovsky

2016

Phys. Rev. E

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The chemomechanical model of Huxley and Simmons (HS) [A. F. Huxley and R. M. Simmons, Nature 233, 533 (1971)NATUAS0028-083610.1038/233533a0] provides a paradigmatic description of mechanically induced collective conformational changes relevant in a variety of biological contexts, from muscles power stroke and hair cell gating to integrin binding and hairpin unzipping. We develop a statistical mechanical perspective on the HS model by exploiting a formal analogy with a paramagnetic Ising model. We first study the equilibrium HS model with a finite number of elements and compute explicitly its mechanical and thermal properties. To model kinetics, we derive a master equation and solve it for several loading protocols. The developed formalism is applicable to a broad range of allosteric systems with mean-field interactions.

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“…The inserts in Figs. 17(a) and 17(b) show samples of the trajectories for single elements computed from (21).…”

Section: B Bundle Of Hs Elementsmentioning

confidence: 99%

Section: Nonmuscle Systemsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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Statistical mechanics of the Huxley-Simmons model

Caruel

Truskinovsky

2016

Phys. Rev. E

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“…A more complex but related example is provided by the "fracture" avalanches during unfolding of macro-molecules (Srivastava and Granek, 2013). The broad applicability of the proposed mechanical perspective is also corroborated by the fact that proteins and nucleic acids behave differently in isometric and isotonic conditions and that these mechanical systems can exhibit negative stiffness (Gerland et al, 2003;Bornschlögl and Rief, 2006;Thomas and Imafuku, 2012). In the same vein, the importance of the topology of interconnections among the bonds and the link between the cooperativity of unfolding and the dominance of parallel bonding have been long stressed in the studies of protein folding (Dietz and Rief, 2008).…”

Section: Discussionmentioning

confidence: 82%

“…Passive collective effects are usually revealed through synchronized conformational changes interpreted here as generic folding-unfolding transitions. The experiment shows that such systems exhibit coherent macroscopic hopping between folded and unfolded configurations resisting the destabilizing effect of finite temperatures (Dietz and Rief, 2008;Thomas and Imafuku, 2012;Erdmann et al, 2013).…”

Section: Introductionmentioning

confidence: 97%

Mechanics of collective unfolding

Caruel

Allain

Truskinovsky

2015

Journal of the Mechanics and Physics of Solids

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Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and structure of the folding-unfolding energy barriers in the hard (fixed displacements) and soft (fixed forces) loading devices which persists in the continuum limit. We argue that both, the synchronization and the non-equivalence of the mechanical responses in hard and soft devices, have their origin in the dominance of long-range interactions. We then apply our minimal model to skeletal muscles where the power-stroke in acto-myosin crossbridges can be interpreted as passive folding. A quantitative analysis of the muscle model shows that the relative rigidity of myosin backbone provides the long-range interaction mechanism allowing the system to effectively synchronize the power-stroke in individual crossbridges even in the presence of thermal fluctuations. In view of the prototypical nature of the proposed model, our general conclusions pertain to a variety of other biological systems where elastic interactions are mediated by effective backbones

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